According to the U.S. Census Bureau, the county has a total area of 550 square miles (1,400 km2), of which 547 square miles (1,420 km2) is land and 2.8 square miles (7.3 km2) (0.5%) is water.
Atchison's western boundary for the most part is the Missouri River and Nebraska. An 1867 flood straightened a bend in the river north of Watson. Both Nebraska and Missouri claimed the 5,000 acre McKissick Island that extends almost two miles into Atchison County. The Supreme Court in 1904 decided that the land belongs to Nebraska. The only way Nebraska can reach it by road is to cross the Missouri River and then travel through Missouri.
As of the census of 2000, there were 6,430 people, 2,722 households, and 1,777 families residing in the county. The population density was 12 people per square mile (5/km²). There were 3,103 housing units at an average density of 6 per square mile (2/km²). The racial makeup of the county was 97.00% White, 2.05% Black or African American, 0.19% Native American, 0.14% Asian, 0.31% from other races, and 0.31% from two or more races. Approximately 0.67% of the population were Hispanic or Latino of any race.
There were 2,722 households out of which 26.60% had children under the age of 18 living with them, 55.80% were married couples living together, 6.10% had a female householder with no husband present, and 34.70% were non-families. 31.50% of all households were made up of individuals and 17.60% had someone living alone who was 65 years of age or older. The average household size was 2.25 and the average family size was 2.82.
In the county the population was spread out with 24.10% under the age of 18, 6.50% from 18 to 24, 24.20% from 25 to 44, 24.20% from 45 to 64, and 21.10% who were 65 years of age or older. The median age was 42 years. For every 100 females there were 99.30 males. For every 100 females age 18 and over, there were 91.90 males.
The median income for a household in the county was $30,959, and the median income for a family was $38,279. Males had a median income of $27,468 versus $18,855 for females. The per capita income for the county was $16,956. About 9.30% of families and 11.60% of the population were below the poverty line, including 13.70% of those under age 18 and 12.40% of those age 65 or over.